How to use ATAC dataset

[Layne-Huang]

Hi,

Thanks for your excellent work. I have downloaded the multiome ATAC + gene expression BMMCs dataset under accession code “GSE194122”. However, I could not find the atac_processed.h5ad and gex_processed.h5ad from a single file GSE194122_openproblems_neurips2021_multiome_BMMC_processed.h5ad in the ATAC related jupyter notebooks. Could you please help me solve it?

Thanks.

[xintangg]

Hi Layne

Sorry, I was not checking this repository recently. The data availability has been described in the "Data Availability" section of our paper: https://www.nature.com/articles/s41467-023-37477-x

Let me know if you have difficulty accessing them and I am happy to help.

Thanks

[AnthonyShea1]

More specifically, the Zenodo data entry holds the files you want to use.

https://zenodo.org/records/7708592#.ZBSIp3Yo9aQ